[gmx-users] Re,i don't know how can i determine emtol

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Fri Nov 23 10:00:27 CET 2012

On 11/22/2012 09:32 PM, Ali Alizadeh wrote:
> 1- In your opinion, Can i simulate that system?
>>>> In my (humble) opinion:
>>>> 1)Of course you can simulate that system...however  I doubt that, without
>>>> starting from the exact initial configuration with the exactly same
>>>> set-up,
>>>> you can get the same results (i.e. see the nucleation).
>>>> The onset of ice nucleation is a random process and requires very long
>>>> simulation (the paper that you posted was analysing micro-second
>>>> trajectories!!).
>>>> There is the risk that you could try several different initial
>>>> configurations at several temperature without getting anything.
>>>>    However, read carefully that paper, I do not remember all the details.
>>>> If you are interested in ice crystal growth, I would suggest to start
>>>> with
>>>> an initial water/ice system: at temperature below the melting one you
>>>> will
>>>> see formation of new ice starting from the initial ice matrix.
>>> I do not know how  can ice crystal in initial step, i study papers and
>>> i know ice , crystals formation and dissociation of crystals is very
>>> difficult,
>>> and we can use this method(as you said above) for melting or
>>> freezing(if i say correct)
>>> My problem is this case, how can i have a crystal in initial step,
>> You have three options
>> 1) Surfing the web searching for some structure.
>> 2)Try to implement the proton disordering algorithm of Buch et al.,
>> (V. Buch, P. Sandler and J. Sadlej, J. Phys. Chem. B, 1998, 102,
>> 8641–8653)
>>   which specifies orientations of water molecules such that ice
>> Ih Bernal–Fowler constraints for each molecule are satisfied.
>> (J. D. Bernal and R. H. Fowler, J. Chem. Phys., 1933, 1, 515–548)
>> 3) Someone kindly offer you his own structure, e.g.
>> http://marge.uochb.cas.cz/~gladich/Teaching.html
> That's right,
> Is it possible that i know how can you construct it?
> You use TIP5P, and i do not know your force field?
> In fact i should  construct this structure by self,
> Can you give some advices so that i can construct it?
I constructed the structure using the method 2) with the Buch's algorithm.
Concerning TIP5P and TIP5P-Ew, here below the references:

1) Mahoney and Jorgensen, J. Chem. Phys., 2000, VOLUME 112, NUMBER 20
2) S. W. Rick, J. Chem. Phys., 2004, 120, 6085–6093.

All the best

Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/

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